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#include <ctype.h>
#include <assert.h>
#include <unistd.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "samtools.pysam.h"
FILE * samtools_stderr = NULL;
FILE * samtools_stdout = NULL;
const char * samtools_stdout_fn = NULL;
int samtools_stdout_fileno = STDOUT_FILENO;
FILE * samtools_set_stderr(int fd)
{
if (samtools_stderr != NULL)
fclose(samtools_stderr);
samtools_stderr = fdopen(fd, "w");
return samtools_stderr;
}
void samtools_unset_stderr(void)
{
if (samtools_stderr != NULL)
fclose(samtools_stderr);
samtools_stderr = fopen("/dev/null", "w");
}
FILE * samtools_set_stdout(int fd)
{
if (samtools_stdout != NULL)
fclose(samtools_stdout);
samtools_stdout = fdopen(fd, "w");
if (samtools_stdout == NULL)
{
fprintf(samtools_stderr, "could not set stdout to fd %i", fd);
}
samtools_stdout_fileno = fd;
return samtools_stdout;
}
void samtools_set_stdout_fn(const char *fn)
{
samtools_stdout_fn = fn;
}
void samtools_unset_stdout(void)
{
if (samtools_stdout != NULL)
fclose(samtools_stdout);
samtools_stdout = fopen("/dev/null", "w");
samtools_stdout_fileno = STDOUT_FILENO;
}
int samtools_puts(const char *s)
{
if (fputs(s, samtools_stdout) == EOF) return EOF;
return putc('\n', samtools_stdout);
}
void samtools_set_optind(int val)
{
// setting this in cython via
// "from posix.unistd cimport optind"
// did not work.
//
// setting to 0 forces a complete re-initialization
optind = val;
}
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